diff --git a/docs/processing.md b/docs/processing.md index 3755e84063de755be4f85c6548600725fb846d30..dc50ac45301d688a0cf7aea37181f190c937ecfb 100644 --- a/docs/processing.md +++ b/docs/processing.md @@ -41,7 +41,10 @@ Here, we provide functionalities designed specifically for 3D image analysis and - maximum - minimum - tophat - - Pipeline +::: qim3d.filters.Pipeline + options: + members: + - append ::: qim3d.features options: diff --git a/qim3d/features/_common_features_methods.py b/qim3d/features/_common_features_methods.py index 42ad89d1a250048966f38825171f53f5e8ef743f..afac05f23046a6e52307d1d9ea0f47501fdfe4b1 100644 --- a/qim3d/features/_common_features_methods.py +++ b/qim3d/features/_common_features_methods.py @@ -25,8 +25,8 @@ def volume(obj, **mesh_kwargs) -> float: mesh = qim3d.io.load_mesh('path/to/mesh.obj') # Compute the volume of the mesh - vol = qim3d.features.volume(mesh) - print('Volume:', vol) + volume = qim3d.features.volume(mesh) + print('Volume:', volume) ``` Compute volume from a np.ndarray: diff --git a/qim3d/generate/_aggregators.py b/qim3d/generate/_aggregators.py index dbba4e53492a444ddef429918a531ce33e370aed..535ad9db66f92d477555c8c804baf29bb5dc7b93 100644 --- a/qim3d/generate/_aggregators.py +++ b/qim3d/generate/_aggregators.py @@ -189,10 +189,10 @@ def noise_object_collection( # Generate synthetic collection of objects num_objects = 15 - synthetic_collection, labels = qim3d.generate.noise_object_collection(num_objects = num_objects) + vol, labels = qim3d.generate.noise_object_collection(num_objects = num_objects) # Visualize synthetic collection - qim3d.viz.volumetric(synthetic_collection) + qim3d.viz.volumetric(vol) ``` <iframe src="https://platform.qim.dk/k3d/synthetic_collection_default.html" width="100%" height="500" frameborder="0"></iframe> @@ -213,7 +213,7 @@ def noise_object_collection( import qim3d # Generate synthetic collection of dense objects - synthetic_collection, labels = qim3d.generate.collection( + vol, labels = qim3d.generate.collection( min_high_value = 255, max_high_value = 255, min_object_noise = 0.05, @@ -224,7 +224,7 @@ def noise_object_collection( max_gamma = 0.02) # Visualize synthetic collection - qim3d.viz.vol(synthetic_collection) + qim3d.viz.vol(vol) ``` <iframe src="https://platform.qim.dk/k3d/synthetic_collection_dense.html" width="100%" height="500" frameborder="0"></iframe> diff --git a/qim3d/generate/_generators.py b/qim3d/generate/_generators.py index 5cab885d803368e834b576bad1d5090216b7f253..cd914696115dd5dd56719e360ef50bb2a814c421 100644 --- a/qim3d/generate/_generators.py +++ b/qim3d/generate/_generators.py @@ -43,16 +43,16 @@ def noise_object( import qim3d # Generate synthetic blob - synthetic_blob = qim3d.generate.noise_object(noise_scale = 0.015) + vol = qim3d.generate.noise_object(noise_scale = 0.015) # Visualize 3D volume - qim3d.viz.volumetric(synthetic_blob) + qim3d.viz.volumetric(vol) ``` <iframe src="https://platform.qim.dk/k3d/synthetic_blob.html" width="100%" height="500" frameborder="0"></iframe> ```python # Visualize slices - qim3d.viz.slices_grid(synthetic_blob, value_min = 0, value_max = 255, num_slices = 15) + qim3d.viz.slices_grid(vol, value_min = 0, value_max = 255, num_slices = 15) ```  diff --git a/qim3d/operations/_common_operations_methods.py b/qim3d/operations/_common_operations_methods.py index 95e36928b92e60f2a6703835a004c664b97abed5..f266173eb5bf97658b5c6ef6b2144a4299cc0bd5 100644 --- a/qim3d/operations/_common_operations_methods.py +++ b/qim3d/operations/_common_operations_methods.py @@ -81,7 +81,7 @@ def fade_mask( Example: ```python import qim3d - vol = qim3d.io.load('yourVolume.tif') + vol = qim3d.io.load('heartScan.tif') qim3d.viz.volumetric(vol) ``` Image before edge fading has visible artifacts from the support. Which obscures the object of interest. diff --git a/qim3d/processing/_local_thickness.py b/qim3d/processing/_local_thickness.py index 8a3814ea04c0dd3144faa147d45a27c93d0ae8b5..c4920dbf6e1dc8d339cb340c76a3d72f20a5553a 100644 --- a/qim3d/processing/_local_thickness.py +++ b/qim3d/processing/_local_thickness.py @@ -40,8 +40,8 @@ def local_thickness( ```python import qim3d - fly = qim3d.examples.fly_150x256x256 # 3D volume - lt_fly = qim3d.processing.local_thickness(fly, visualize=True, axis=0) + vol = qim3d.examples.fly_150x256x256 + lt_vol = qim3d.processing.local_thickness(vol, visualize=True, axis=0) ```  @@ -49,11 +49,10 @@ def local_thickness( import qim3d # Generate synthetic collection of blobs - num_objects = 15 - synthetic_collection, labels = qim3d.generate.noise_object_collection(num_objects = num_objects) + vol, labels = qim3d.generate.noise_object_collection(num_objects=15) # Extract one slice to show that localthickness works on 2D slices too - slice = synthetic_collection[:,:,50] + slice = vol[:,:,50] lt_blobs = qim3d.processing.local_thickness(slice, visualize=True) ```